|
| Status |
Public on Feb 15, 2023 |
| Title |
674M |
| Sample type |
SRA |
| |
|
| Source name |
maxillary process cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: maxillary process cells
chip antibody: Dlx2 (Abcam, #ab272902)
|
| Growth protocol |
C57BL/6 mice were purchased from Shanghai Jihui Laboratory Animal Care Co.Ltd. All mice were maintained in SPF conditions at the Animal Center of the Ninth People’s hospital affiliated to Shanghai Jiaotong University School of medicine. Female and male mice between the ages of 8 to 12 weeks were used.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq X following the manufacturer's protocols.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
Dlx2 CUT&Tag of E12.5 maxillary process tissue in wildtype mice
|
| Data processing |
Raw data were trimmed from 3' end until the final base had a quality score > 30, using Trimgalore-0.4.5, discarding reads left with < 20 bp
Raw data were aligned to the UCSC mm10 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS2 v2.2.7 with the significance cut-off q-value <=0.01
Assembly: mm10
Supplementary files format and content: narrowPeak
Library strategy: CUT&Tag
|
| |
|
| Submission date |
Nov 03, 2022 |
| Last update date |
Feb 18, 2023 |
| Contact name |
Jian Sun |
| E-mail(s) |
orthodoc_sun@hotmail.com
|
| Phone |
021-15821965892
|
| Organization name |
Shanghai Ninth People's Hospital
|
| Street address |
Quxi Road No.500
|
| City |
Shanghai |
| ZIP/Postal code |
200011 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (2) |
| GSE217212 |
Effects of Dlx2 Overexpression on the Genome of Maxillary Process in Early Embryo of Mice [CUT&Tag] |
| GSE217214 |
Effects of Dlx2 Overexpression on the Genome of Maxillary Process in Early Embryo of Mice |
|
| Relations |
| BioSample |
SAMN31592076 |
| SRA |
SRX18157815 |
